Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication

Controversies in modern evolutionary biology: the imperative for error detection and quality control

(2012) Francisco Prosdocimi et al.   BMC GENOMICS

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution

(2012) Robert K. Bradley et al.   PLOS BIOLOGY

Domain Loss Facilitates Accelerated Evolution and Neofunctionalization of Duplicate Snake Venom Metalloproteinase Toxin Genes

(2011) N. R. Casewell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Error and Error Mitigation in Low-Coverage Genome Assemblies

(2011) Melissa J. Hubisz et al.   PLoS One

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms

(2011) Alinda Nagy et al.   Genes

Important role of indels in somatic mutations of human cancer genes

(2010) Haiwang Yang et al.   BMC Medical Genetics

Impact of Indels on the Flanking Regions in Structural Domains

(2010) Zheng Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Different Phylogenomic Approaches to Resolve the Evolutionary Relationships among Model Fish Species

(2010) E. Negrisolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extensive Divergence in Alternative Splicing Patterns after Gene and Genome Duplication During the Evolutionary History of Arabidopsis

(2010) P. G. Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic interactions reveal the evolutionary trajectories of duplicate genes

(2010) Benjamin VanderSluis et al.   Molecular Systems Biology

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

(2010) Donald F Conrad et al.   NATURE GENETICS

The Combined Effects of Amino Acid Substitutions and Indels on the Evolution of Structure within Protein Families

(2010) Zheng Zhang et al.   PLoS One

Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict

(2010) C. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative

(2009) Baocheng Guo et al.   GENE

Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates

(2009) K. S. Kassahn et al.   GENOME RESEARCH

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study

(2009) Fereydoun Hormozdiari et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

(2009) J.-Q. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants

(2009) J. D. Hollister et al.   MOLECULAR BIOLOGY AND EVOLUTION

Heterogeneous Patterns of Gene-Expression Diversification in Mammalian Gene Duplicates

(2009) D. Farre et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomewide Association between Insertions/Deletions and the Nucleotide Diversity in Bacteria

(2009) L. Zhu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Protein structure homology modeling using SWISS-MODEL workspace

(2009) Lorenza Bordoli et al.   Nature Protocols

Duplicate genes increase expression diversity in closely related species and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryptic Variation in the Human Mutation Rate

(2009) Alan Hodgkinson et al.   PLOS BIOLOGY

Identifying protein-coding genes in genomic sequences

(2009) Jennifer Harrow et al.   GENOME BIOLOGY

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

(2008) Alinda Nagy et al.   BMC BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

(2008) R. A. Studer et al.   GENOME RESEARCH

Evolutionary pattern of protein architecture in mammal and fruit fly genomes

(2008) Haiwang Yang et al.   GENOMICS

Selection on Length Mutations After Frameshift Can Explain the Origin and Retention of the AP3/DEF-Like Paralogues in Impatiens

(2008) Steven B. Janssens et al.   JOURNAL OF MOLECULAR EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The pattern of insertion/deletion polymorphism in Arabidopsis thaliana

(2008) Wen Zhang et al.   MOLECULAR GENETICS AND GENOMICS

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

(2008) Dacheng Tian et al.   NATURE

Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila

(2008) Shuang Yang et al.   PLoS Genetics

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY